Bacterial mRNA screen strategy for novel pesticide-encoding nucleic acid molecule discovery - Methods are provided for isolating and identifying novel pesticide-encoding nucleic acid molecules from bacterial strains identified as having a pesticidal polypeptide. The methods involve selecting a bacterial strain having or suspected of having at least one pesticide-encoding plasmid, curing the at least one pesticide-encoding plasmid from the bacterial strain and performing a subtractive hybridization to obtain plasmid mRNA encoding the pesticidal polypeptide. The plasmid mRNA can be used to make a cDNA library from which the pesticidal polypeptide can be isolated and subsequently identified.